Sometimes alpha helices have segments of 3/10 helix at the end. In the transition area, there are residues for which the amide N is equally close to the carbonyl oxygens of the residues 3 and 4 before, and carbonyl O are equally close to amide N's 3 or 4 residues ahead. The carbonyl O has two lone pairs and presumably could bind to both if the geometry is right, but could the amide N, with one H, bond to two carbonyl groups? If so this could allow a smooth transition from alpha helix to 3/10 as a helix is stretched- with the alpha helical bonds getting longer and weaker while the 3/10 bonds are forming and taking over, until eventually there are strong ideal 3/10 bonds and the alpha bonds are stretched out of existence.
Hi Ed, - interesting question, - I'll contact you directly about a context!
Tony
Hello Edward
What you find in experimentally determined structures will depend to some extent on your criteria for identifying of a hydrogen bond. Bifurcated hydrogen bonds are not uncommon outside the cores of regular secondary structures. If I recall correctly from an old publication, 3.10 and pi connections occur less than 5% at the ends of alpha helices (Kabsch and Sander,1983).
I attach a picture I prepared of some ideal 20 residue helices in alpha, pi and 3.10 to appreciate the difference in length of these structures (from a chapter I wrote for the Principles of Protein Structure course).
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